I can run motion fine from the command line and see video on port 8081, but I have the following problems:

1) I don't know where to copy the motion program to so that it sits in the 'correct' place for auto start on boot up - and it doesn't start on boot. When I tried to use the cp command to copy it to /usr/bin/motion the source file disappeared (!!!) - is that normal for cp? And should it be at /usr/bin/motion ?

2) I can't seem to get any log files written, though I have specified the location, touched and chmodded accordingly...

3) I can't seem to get motion to accept better resolution than 640x480. Is that normal?

I have never been happy with changing the binaries in /usr. Either it gets overwritten in an update, or I get confused about which version or which config file it is actually using. I also don't use the daemon mode of motion. So I copy my config file to my home directory, then test motion (while tweaking the config file) by running this: (Motion spits out useful debugging logs directly to the terminal)

Now motion is started (as user pi) at startup and uses the right binary and config. The log messages are now sent automatically to /var/log/syslog.

Your resolution question is a bit more complicated. The clever part of this version of motion is that the Pi's camera feeds low resolution video to the motion detection algorithm - so that the Pi's processor isn't too heavily loaded - and at the same time, higher resolution stills and videos of the detected movement can be saved. So you need to have a good look at your config file to get the resolution you want. These are the key lines in the config

Pi's camera feeds low resolution video to the motion detection algorithm - so that the Pi's processor isn't too heavily loaded - and at the same time, higher resolution stills and videos of the detected movement can be saved

Is something I am very interested in. Can you help me understand how to implement this?